High-density sequence tagged sites (STS, 10/Mb) are being produced by the single pass sequencing of high purity flow-sorted small insert libraries at the Sanger Centre. The STSs are mapped using radiation hybrids to produce an accurate physical map of the markers; the mapped STSs are used to screen a 15X genomic PAC library to generate a minimal overlapping set of PAC clones for sequencing. In collaboration with the Sanger Centre we are investigating whether a significant increase in the efficiency of this process can be generated by using high-purity chromosome-specific rather than genomic PAC libraries as the clone source for sequencing. As size-selection of partially digested DNA is required for the construction of a PAC library containing inserts of over 100kb, many micrograms of flow-sorted chromosome material are required. This quantity of flow sorted chromosomes is prohibitive to produce using conventional flow sorting. The optical sorter under development by the NFCR will be used to meet these needs.